- Research article
- Open Access
Molecular phylogeny of pearl oysters and their relatives (Mollusca, Bivalvia, Pterioidea)
© Tëmkin; licensee BioMed Central Ltd. 2010
- Received: 15 July 2010
- Accepted: 8 November 2010
- Published: 8 November 2010
The superfamily Pterioidea is a morphologically and ecologically diverse lineage of epifaunal marine bivalves distributed throughout the tropical and subtropical continental shelf regions. This group includes commercially important pearl culture species and model organisms used for medical studies of biomineralization. Recent morphological treatment of selected pterioideans and molecular phylogenetic analyses of higher-level relationships in Bivalvia have challenged the traditional view that pterioidean families are monophyletic. This issue is examined here in light of molecular data sets composed of DNA sequences for nuclear and mitochondrial loci, and a published character data set of anatomical and shell morphological characters.
The present study is the first comprehensive species-level analysis of the Pterioidea to produce a well-resolved, robust phylogenetic hypothesis for nearly all extant taxa. The data were analyzed for potential biases due to taxon and character sampling, and idiosyncracies of different molecular evolutionary processes. The congruence and contribution of different partitions were quantified, and the sensitivity of clade stability to alignment parameters was explored.
Four primary conclusions were reached: (1) the results strongly supported the monophyly of the Pterioidea; (2) none of the previously defined families (except for the monotypic Pulvinitidae) were monophyletic; (3) the arrangement of the genera was novel and unanticipated, however strongly supported and robust to changes in alignment parameters; and (4) optimizing key morphological characters onto topologies derived from the analysis of molecular data revealed many instances of homoplasy and uncovered synapomorphies for major nodes. Additionally, a complete species-level sampling of the genus Pinctada provided further insights into the on-going controversy regarding the taxonomic identity of major pearl culture species.
- Pearl Oyster
- Hinge Line
- Alignment Parameter
- Outgroup Taxon
- Doubly Uniparental Inheritance
Since the lower Middle Ordovician some 470 million years ago, pterioidean bivalves have inhabited a remarkable diversity of marine epifaunal and semi-infaunal environments around the globe, typically confined to cryptic habitats and forming byssal attachments to various substrata. For a much shorter part of their history-from the dawn of human culture-they have become the primary source of pearls and nacre [1–3]. Pearl fishing based on natural populations of pterioidean bivalves had expanded into a growing global industry with a current value of approximately half a billion US dollars per annum . In pursuit of pearls, commercial introductions and accidental transport of pterioideans beyond their native distribution ranges have greatly affected population dynamics of some species endangering local indigenous biotas (e.g., [5–8]). A recent interest in physical properties of mother-of-pearl made pterioidean bivalves a model system for elucidating molecular mechanisms of biomineralization with medical applications for bone regeneration (e.g., [9, 10]). Given the long and many-sided history of pterioideans and humans, and the current economic and ecological significance of these bivalves, surprisingly little is known about the standing alpha-diversity, distribution, and evolutionary history of the group.
The present-day diversity of the superfamily Pterioidea Gray, 1847  encompasses four families traditionally defined by shell shape and ligament structure: Pteriidae, Isognomonidae, Malleidae, and Pulvinitidae [12–15]. Pteriids are distinguished by an obliquely ovate shell shape, an enlarged posteriorly projecting auricle, and a deep byssal notch. Many pteriid species, particularly of genera Pteria and Electroma, evolved specialized associations with hydroid, scleractinian, and alcyonarian substrata. Most species of Pinctada (pearl oysters) inhabit sandy and hard bottoms, some living in association with commensal fishes and crustaceans. Several species of Pteria and Pinctada are cultured for commercial pearl production. Most species of a malleid genus Malleus are irregularly shaped to conform to narrow crevices in hard coral and rocky substrata, and develop elongated extensions of the hinge for stabilization in soft sediment. Species of the second malleid genus, Vulsella, are adapted for living within sponges. Isognomonids are characterized by the distinct morphology of the ligament that contains multiple grooves (resilifers) for ligamental attachments arranged sequentially along the hinge line (multivincular ligament). Species of the genus Isognomon often co-occur with species of Malleus in crevices and on soft muddy bottoms, but also are gregarious on mangrove roots, whereas species of Crenatula, the second isognomonid genus, live inside sponges (as the malleid Vulsella). Similarly to isognomonids, pulvinitids possess multivincular ligament, but are distinguished from isognomonids by the presence of the foramen, an opening in the right valve through which the byssus is protruded. Living pulvinitids are represented by the genus Pulvinites, the sole extant species of which, Pulvinites exempla, lives byssally attached to vertical hard substrata at 200-400 m depths.
Previous studies aimed at resolving higher-level phylogeny within Bivalvia agreed on the monophyly of the Pterioidea and its placement within the subclass Autolamellibranchiata. However, most aspects of relationships within the superfamily and the identity of its immediate sister group remain uncertain. In a pioneering study on the evolution and ontogeny of the bivalve shell, Jackson (1890) proposed the derivation of major pterioidean groups from a Pteria¬-like Paleozoic ancestor . In his scheme, several autolamellibranchiate lineages, including common oysters of the family Ostreidae and several extinct families, evolved from Isognomon, the latter ultimately arising from the Pteria stem lineage. Jackson also provisionally recognized close relatedness of Malleus and Vulsella.
In summary, molecular studies, varying greatly in sampling and analytical techniques, produced inconsistent hypotheses of pterioidean relationships with low resolution and support. These findings, however, agreed on the monophyly of the superfamily and suggested that the families Pteriidae and Malleidae were not monophyletic. The results were conflicting with regard to the monophyly of the genera Pteria and Pinctada, whereas Isognomon was invariably monophyletic. The monophyly of the family Isognomonidae and the genera Electroma and Malleus were not tested, and representatives of the family Pulvinitidae and the genus Crenatula were not included in the analyses. The only study that focused exclusively on the Pterioidea was based on morphological characters and included representatives of all four families and nine genera (Figure 1f) . It supported the monophyly of the Pterioidea and non-monophyly of three families (Pulvinitidae remains untested being represented by a single extant species). All the genera that were represented by multiple species (Pteria, Pinctada, Isognomon, and Malleus) were recovered monophyletic. Species-level sampling in that study was insufficient to test the assumption of monophyly of the remaining genera and did not include type species for most nominal supraspecific taxa. Despite these recent challenges on both molecular and morphological grounds, no consensus on pterioidean relationships was reached and no revision of the existing classification was proposed.
The identity of the pterioidean sister group remains uncertain, favoring the oysters (Ostreoidea), pen shells (Pinnoidea), or a clade composed of these two groups, currently classified together with the Pterioidea in the order Pterioida. Most analyses based on morphological data for extinct, extant, or both kinds of taxa, have suggested a sister relationship of the Pterioidea and Pinnoidea [20–24], except for one, which instead suggested a closer relationship of the Pterioidea and Ostreoidea . Likewise, molecular analyses were divided in favoring either Pinnoidea  or Ostreoidea [18, 19, 26] as a sister group of the Pterioidea. In other studies, either Pinnoidea and Ostreoidea formed a clade sister to the Pterioidea [17, 19], or the relationships among the three superfamilies were unresolved [25, 27]. The only explicitly combined analysis of morphological and molecular data resolved the Pinnoidea basal to the Pterioidea/Ostreoidea clade . The unsettled question of the pterioidean sister group is pertinent to the recent debates on the origin of oysters in paleontological literature [28–30].
The present analysis is the first study to produce a nearly comprehensive species-level phylogeny for the Pterioidea based on DNA sequence data. The principal specific goals of this study include (1) testing the monophyly of the Pterioidea, and all its families and genera; (2) reviewing the consequences of these results for the homology of important morphological characters; and (3) resolving species-level phylogenetic relationships within the commercially important pearl oyster genus Pinctada.
Sources of specimens
Specimen and DNA sequence sources.
GenBank Acc. No. (18S/28S/16S/H3)
Florida Keys, USA
Florida Keys, USA
Florida Keys, USA
Pinctada albina 1
Pinctada albina 2
The Amami Islands, Japan
Pinctada albina 3
Northern Territory, Australia
Pinctada capensis 1
Pinctada capensis 2
Pinctada capensis 3
Pinctada fucata 1
The Amami Islands, Japan
Pinctada fucata 2
Kamikoshiki island, Japan
Pinctada fucata 3
Pinctada fucata 4
Pinctada fucata 5
Pinctada fucata 6
Pinctada fucata 7
Japan [pearl farm]
Pinctada fucata 8
Pinctada fucata 9
Pinctada fucata 10
Pinctada imbricata 1
Pinctada imbricata 2
Florida Keys, USA
Pinctada imbricata 3
Florida Keys, USA
Pinctada imbricata 4
Florida Keys, USA
Pinctada longisquamosa 1
Florida Keys, USA
Pinctada longisquamosa 2
Florida Keys, USA
The Amami Islands, Japan
Pinctada margaritifera 1
Pinctada margaritifera 2
Pinctada nigra 1
Pinctada nigra 2
The Amami Islands, Japan
Pinctada nigra 3
Northern Territory, Australia
Pteria avicular 1
Bohol Island, Philippines
Pteria avicular 2
Bay of Bengal, India
Pteria avicular 3
Pteria avicular 4
Bohol Island, Philippines
Pteria avicular 5
Pteria avicular 6
Pteria colymbus 1
Pteria colymbus 2
Mediterranean Sea, Italy
Pteria howensis 1
Bohol Island, Philippines
Pteria howensis 2
Bohol Island, Philippines
Pteria howensis 3
Norfolk Island, Australia
Pteria lata 1
Darwin Harbour, Australia
Pteria lata 2
Pteria penguin 1
Panglao Island, Philippines
Pteria penguin 2
Raffles Bay, Australia
Electroma alacorvi 1
Electroma alacorvi 2
Balicasag Island, Philippines
Electroma cf. alacorvi 1
Houtman Abrolhos, Australia
Electroma cf. alacorvi 2
Houtman Abrolhos, Australia
Electroma cf. alacorvi 3
Houtman Abrolhos, Australia
Raffles Bay, Australia
Florida Keys, USA
Florida Keys, USA
Darwin Harbor, Australia
Isognomon cf. ephippium A1
Koh Nam Sao Island, Thailand
Isognomon cf. ephippium A2
Koh Nam Sao Island, Thailand
Isognomon cf. ephippium B
Kungkrabaen Bay, Thailand
Isognomon isognomum 1
Chong Saba Island, Thailand
Isognomon isognomum 2
Isognomon isognomum 3
Panglao Island, Philippines
Isognomon isognomum 4
Koh Nam Sao Island, Thailand
Isognomon isognomum 5
Koh Nam Sao Island, Thailand
Isognomon isognomum 6
Kungkrabaen Bay, Thailand
Isognomon isognomum 7
Kungkrabaen Bay, Thailand
Florida Keys, USA
Kungkrabaen Bay, Thailand
Isognomon sp. A1
Houtman Abrolhos, Australia
Isognomon sp. A2
Noumea, New Caledonia
Kungkrabaen Bay, Thailand
Malleus cf. albus 1
Rottnest Island, Australia
Malleus cf. albus 2
Houtman Abrolhos, Australia
Malleus cf. albus 3
Houtman Abrolhos, Australia
Florida Keys, USA
Bohol Island, Philippines
Malleus regula 1
Darwin Harbor, Australia
Malleus regula 2
Darwin Harbor, Australia
Malleus regula 3
Panglao Island, Philippines
Kungkrabaen Bay, Thailand
Vulsella cf. vulsella
East Cape, New Zealand
Given that the Pterioidea is currently accepted as monophyletic and the Pinnoidea or Ostreoidea were established as the taxa most closely related to the Pterioidea on morphological and molecular grounds, representatives of these superfamilies were chosen for the outgroup. To ensure maximum diversity of the ostreoidean taxa, the selection of the gryphaeid Hyotissa, and the ostreid Ostrea and Crassostrea exemplars were guided by their placement in a recently proposed phylogenetic hypothesis . To polarize the immediate outgroups, representatives of two other autolamellibranchiate orders, Mytiloida and Pectinoida were selected based upon the availability of sequence data. Mytilioda, represented by the well-known common mussel species, Mytilus edulis, had been resolved as the most basal order of the subclass in comprehensive studies based on morphological , molecular [18, 24], and combined  data and, accordingly, was designated for cladogram rooting.
Inasmuch as the Pterioidea is the primary focus of this study, the taxonomic sampling of this taxon was the most dense. All nominal families and genera of the Pterioidea were included in the analyses. The sample contained representatives of type species of all pterioidean genera except for Pulvinites, which was described based on an extinct species, P. adansonii, from the Late Cretaceous. Success in securing multiple representatives for each genus varied because the material could not be obtained for few taxa characterized by cryptic life habit and presumed low species diversity. Initially, specimens were sorted to morphospecies using anatomical and shell morhological features. Species-level identifications were verified with reference to the extant type material and assigned to most specimens. Where possible, to avoid assumptions of the extent of intraspecific phenotypic variation, multiple potentially conspecific individuals were included in the analysis. Given the lack of recent systematic revisions for the majority of pterioidean taxa, species-level identifications were tentatively chosen with correspondence to their prevailing use in current literature.
The sample of the genus Pinctada was complete, with 32 exemplars representing 10 nominal species, including the type species Pinctada margaritifera. The overrepresentation of Pinctada species was necessitated by an enduring controversy regarding the taxonomic status of the Pinctada imbricata/fucata/radiata species complex  that includes important perliculture species. Sampling of Pteria was nearly comprehensive; it included 18 exemplars of 10 nominal species (including the type species Pteria hirundo) of estimated total of 12 species. The genus Isognomon was represented by 18 exemplars corresponding to potentially 10 of approximately 13 species total, and includes the type species, I. isognomum. The genus Malleus was represented by 9 exemplars, corresponding to 5 (of total approximately 8) species, including Malleus malleus, the type species of the genus, and Malleus regula, a type species of the subgenus Malvufundus. It must be pointed out that the true global species diversity of Isognomon and Malleus is not known due to potential high endemism and cryptic diversity associated with adaptations to hidden habitats, such as interstitial crevices and submarine caves. The extent of species coverage for the relatively rare and inadequately studied genera Vulsella, Crenatula, and Electroma is uncertain due to cryptic lifestyle in coral crevices and inside sponges. A broad survey based on dry shells from over twenty major museum collections worldwide suggested that these genera contain very few species and that Crenatula is likely to be monotypic. The latter was represented in the analysis by a single specimen corresponding to the type species, C. avicularis (previously used in the morphology-only phylogenetic analysis under the synonym C. modiolaris ). The genus Electroma was represented by seven exemplars corresponding to potentially four species, including E. alacorvi and Electroma (Pterelectroma) physoides [commonly referred to by its junior synonym, E. (P.) zebra], the sole living member of the subgenus. Two exemplars of Vulsella, corresponding to the type species V. vulsella, one of possibly only two living species, were included in the analysis. The genus Pulvinites was represented by one exemplar of the only extant pulvinitid species, P. exempla.
Genome-wide sampling of multiple independently evolving genes is instrumental in overcoming the incongruence among trees derived from individual gene analyses, and producing a resolved and strongly supported phylogeny. Because this study involves the analysis of taxa of disparate levels of divergence, a data set was assembled that consisted of nuclear loci (two ribosomal RNA genes and the histone H3) and a mitochondrial ribosomal RNA locus, that in combination span a broad spectrum of variation. The ribosomal DNA sequences display a substantial difference in evolutionary rates among and within the genes (from fast-evolving mitochondrial to the much more conserved nuclear rDNA), and are easily amplifiable due to the presence of multiple copies per genome and the pattern of concerted evolution . The following DNA regions were used: (1) the complete sequence of the small nuclear ribosomal subunit (SSU or 18S rDNA; range 1237-1778 bp; total aligned length 1882 bp); (2) the D1-D3 fragments of the large nuclear ribosomal subunit (LSU or 28S rDNA; range 308-1131 bp; total aligned length 1308 bp); (3) a fragment of the large mitochondrial ribosomal subunit (mtLSU or 16S rDNA; range 466-580 bp; total aligned length 934 bp), and (4) the single-copy nuclear histone gene H3 (the total length 310 bp), which is intron-free and highly conserved at the level of amino acids. The total length of the alignment of the complete data set was 4434 bp.
DNA isolation and amplification
Sources and sequences of forward (F) and reverse (R) primers.
Sequence, 5' - 3'
Sequence fragments were assembled into contigs, and checked for errors and ambiguities against chromatograms using Sequencher™ 4.6 (Gene Codes). The sequence coverage varied from 2× to 6× depending on the quality of the material. The resultant sequences were checked for potential contamination by BLAST searches [34, 35] as implemented by the NCBI website http://www.ncbi.nlm.nih.gov. The new sequences have been deposited in GenBank under accession numbers HQ329247-HQ329509 (Table 1).
DNA sequence homology
The ribosomal DNA sequences, the principal source of character data in the present study, vary considerably in length, creating uncertainty in the inference of nucleotide-level homology. To circumvent alignment ambiguity, all potential nucleotide homologies were evaluated in the framework of dynamic homology [36, 37], as implemented in POY 4.1 . In this approach nucleotide correspondences (putative positional homologies) and their transformations (substitutions and insertion-deletion events) are simultaneously optimized for each tree topology provided an optimality criterion and a cost function (transformation step matrix). The integration of alignment and tree searching into a single procedure to produce globally optimal trees allows for evaluating multiple unique homology schemes on a consistent theoretical basis, as both are evaluated using the same criteria [39, 40]. In simultaneous analysis using direct optimization, morphological and molecular characters are co-optimized at the level of sequence alignment in search of a globally optimal solution. The homology scheme corresponding to the topology of the optimal cladogram was used to produce an implied alignment [41, 42]. The implied alignment was used for statistical tests of sequence variation and other analyses requiring fixed character matrices with equal length character strings (i.e. multiple alignments).
DNA sequences were partitioned into fragments to reduce computation time and to constrain the assignment of insertions and deletions (indels) to unambiguously homologous regions. None of the regions were excluded from the analyses except for the flanking primer sequences. Initially, multiple alignments were constructed using ClustalX 2.0.5  under default parameter settings. For rDNA sequences, the alignments were subsequently partitioned into fragments flanked by highly conservative (lacking indels) regions corresponding to elements of secondary structure. The secondary structure features were identified with reference to those inferred for molluscan [44, 45] and other metazoan (e.g., [46–50]) taxa. Lastly, the gaps were removed resulting in a total of 26 matrices of unaligned fragments. All histone H3 sequences had the same length. A comparison of the translated H3 open reading frame with the published database of histone sequences  confirmed high conservation at the level of amino acids. In this case, the nucleotide homology was unambiguous and the H3 data set was treated as a single aligned fragment.
Patterns of nucleotide substitutions
Individual data partitions were tested for substitution saturation using a non-parametric statistical test based on an information entropy index  implemented in DAMBE 5.0.23 . The actual number of transitions and transversions, and their ratio were obtained by optimizing substitutions on the optimal topology using MacClade 4.07 . Departure from homogeneity of base composition across all taxa was assessed using the χ2 test as implemented in PAUP* 4.0d105 . The extent of rate variation across sites for individual data partitions and for the entire data set was estimated by the shape parameter α of the gamma distribution. The values of α were estimated by the maximum likelihood method assuming the discrete gamma model [56, 57] with four rate categories as implemented in PAUP* 4.0d105 .
For close inspection of species-level divergence of the problematic Pinctada imbricata/fucata/radiata species complex, the genetic distances were obtained for within and among presumed species, and then compared to the inter- and intraspecific levels of sequence divergence inferred for their congeners. In this analysis, the distance matrices for rDNA data sets were generated using the minimum evolution objective function (ME; [58, 59]) under the general time-reversible model of nucleotide substitution (GTR; [60–62]) using PAUP* 4.0d105 . The choice of the substitution model was guided by the best-fit model preferred by the Akaike Information Criterion (AIC; ) for the combined molecular data set under maximum likelihood (ML) optimality criterion (see below). The H3 data set was not used in this analysis due to missing data for several critical taxa in question.
A previously published data set based on morphological data  was used for simultaneous analysis of morphological and molecular data. The morphological characters and methods have been described and illustrated in detail in . The data set included 134 morphological characters scored for 19 exemplar species, representing all valid pterioidean genera. As in the original study, all characters were unweighted and one multistate character (the differentiation of gill filaments) was treated as additive based on unequivocal ontogenetic evidence. Molecular data were available for all the taxa for which morphological characters were sampled with the exception of Malleus anatinus. Therefore, for the simultaneous analysis of morphological and molecular data sets, the sequences of a closely related species, M. albus, were used as a surrogate for the missing molecular data for M. anatinus. Given the small number of taxa for which morphological data was available, the benefits of minimizing the amount of missing data at the expense of using a composite taxon was justified in the context of the present analysis aimed primarily at resolving supraspecific relationships. For the morphological character matrix, see .
Character Matrices and Incongruence-Length Difference Tests
Several different molecular data sets varying in taxon and character sampling were examined in the present study. The most comprehensive character matrix (hereafter referred to as the "complete data set") included sequences for four loci scored for 100 exemplars (12 outgroup and 88 ingroup terminal taxa). The complete data set contained representatives of all supraspecific taxa and approximately 92% of all extant species of the Pterioidea. In this data set 43% terminals were represented by sequences for all four loci, 54%-by three loci, 2%-by two loci, and only 1%-by a short fragment of a single locus. Thus, character sampling was not satisfactory for 3% of terminal taxa (the ingroup taxa Pulvinites exempla and Vulsella vulsella, and the outgroup taxon Pinna muricata), and their placement must therefore be treated with caution. The second character matrix (hereafter referred to as the "reduced data set") was restricted to the subset of those taxa for which morphological data was available. The reduced data set was tailored for a combined analysis to have a maximum taxonomic overlap of morphological and molecular character matrices with minimum missing data. This data set contained 19 exemplars (3 outgroup and 16 ingroup terminal taxa), representing all pterioidean genera and families. Morphological data was scored for all 19 terminals; 14 of these terminals had a complete complement of molecular data (4 loci), 4 terminals had sequence data for three loci, and one terminal (Pulvinites exempla) was represented by a single fragment of the 18S locus. The simultaneous analyses of molecular and morphological data were performed under maximum parsimony optimality criterion with the same cost for transformations of morphological characters as for nucleotide substitutions. In addition to the complete and reduced matrices of combined molecular data, five data sets corresponding to the combined nuclear data (18S, 28S, and H3) and the four individual loci (18S, 28S, 16S rDNA, and histone H3) were analyzed in the parsimony framework to explore topological differences, and the extent of resolution and support among the partitions.
To evaluate the degree of incongruence between the data sets quantitatively, the incongruence-length difference tests (ILD; [64–66]) were performed in PAUP* 4.0d105  [but see, e.g., [67, 68] for criticisms of the ILD test]. The ILD tests were done simultaneously on the four individual locus matrices as well as pairwise on the complete data set. The tests were performed under parsimony using 100 replicates, where each replicate consisted of 10 random-addition sequences (RAS), with one tree retained per iteration, followed by tree bisection and reconnection (TBR; ) branch swapping to completion.
Tree searching and optimization
Phylogenetic analyses of DNA sequence data were performed using direct optimization , a heuristic approximation to the optimal tree alignment method [71–75], under parsimony optimality criterion. A heuristic extension of generalized optimization [76, 77], direct optimization includes insertion and deletion events in addition to substitutions as character transformations, allowing for the analysis of sequences of different lengths. Additional analyses based on a static alignment and ML optimality criterion were performed to characterize the patterns of nucleotide substitutions and to explore potential sources of systematic error for inferences based on the assumptions of parsimony. These analyses were based on the implied alignment corresponding to the single optimal cladogram obtained from the parsimony analysis of the combined data performed by direct optimization under the equal-cost regime for the combined molecular character data set.
Parsimony analyses under direct optimization, as implemented in POY 4.1 , were carried out in parallel on the American Museum of Natural History Parallel Computing Cluster and a dual-processor personal computer. A stepwise tree searching strategy that combines independent multiple starting points and efficient algorithms designed for escaping local optima was used to insure sufficient sampling of tree space. Initially, 250-300 Wagner trees [78, 79] were generated by RAS and submitted to branch swapping to completion by alternating rounds of subtree pruning and regrafting (SPR; ) and TBR. The resultant optimal cladograms were subjected to 50 iterations of TBR parsimony ratchet , upweighting 20% of nucleotide characters by a factor of 5 and retaining one optimal cladogram per iteration. In the next step, the optimal cladograms were submitted to tree fusing , allowing for up to 200 pairwise clade exchanges, which was followed by another round of TBR. Finally, the resultant optimal cladograms were submitted to a final round of TBR under exact three-dimensional direct optimization (iterative pass optimization; ), a more efficient, but substantially more computationally intensive method. The final equally most-parsimonious trees (MPTs) were rediagnosed to ensure the correctness of tree length calculation and were used to infer implied alignment. All tree searches were performed with unconstrained ingroup and outgroup designation .
The ML analyses were performed using RAxML 7.0.4  for 250 independent replicates. The results were evaluated for topological congruence and convergence on the optimal likelihood value to ensure that the heuristic searches of tree space were sufficiently thorough. There appears to be no starting-point dependence to successive approximation that could potentially compromise the accuracy of approximation compared to full-optimization of ML searches . The best-fit model of substitution, given the optimal cladogram and the corresponding implied alignment, was selected by Modeltest 3.7  for the combined molecular data set using the Akaike Information Criterion (AIC; [63, 87]). The model favored by the Akaike Information Criterion (AIC = 60431.5938) corresponded to the general time-reversible model that included estimation of the proportion of invariant sites (P-Invar) and assumed a gamma distributed rate variation among sites (GTR + I + Γ). However, due to non-independence of P-Invar and the shape parameter α of the gamma distribution [88, 89], the ML analyses were performed under the GTR + Γ model. Topological differences between the trees based on the partitioned and combined data do not present a problem for choosing among alternative models of sequence evolution, because tree topology does not strongly affect model estimation unless long internal branches are involved .
The ensemble consistency index (CI; ) and the ensemble retention index (RI; [78, 91]) for the optimal tree(s) were calculated in POY 4.1  with the dynamic-homology characters transformed into static nucleotide-level characters by static approximation . The robustness of phylogenetic relationships was evaluated using the Bremer (BrS; ) and jackknife (JK; ) support methods at nucleotide level. Relative contribution of individual genes was assessed by partitioned Bremer support (PBrS; ). The batch files for constrained searches were generated by TreeRot 3 . The constrained searches (100 replicates per search) were performed by PAUP* 4.0d105 . For calculating jackknife support values, 2000 resampling iterations with 36% of sites removed during each pseudoreplicate were performed using POY 4.1 . For the partitioned analyses, only jackknife support values were estimated.
The significance of the length difference between alternative topologies was tested by the Kishino-Hasegawa test using resampling of estimated log-likelihoods (RELL) bootstrap (the KH test; [97, 98]) with 1000 replicates under ML criterion, and the Wilcoxon signed-ranks test (the Templeton test; [99, 100]) and the KH test under parsimony criterion as implemented in PAUP* 4.0d105 . The tests conducted under ML were performed using the GTR + Γ, the same model used for the ML tree searches. The likelihood-based tests are generally considered inapplicable for post-hoc tests of the optimal versus an alternative topology [101, 102]. In the present study, these paired-sites tests were used to assess the significance of alternative outgroup taxon configurations using constrained topologies defined a priori (none of which corresponding to the actual optimal tree) for the reduced molecular data set.
Indel treatment and sensitivity analysis
Because direct optimization integrates the implied alignment and the explicit topology, the choice of analytical parameters (character state transformation weights, or costs, for nucleotide substitutions and indels) is critical for phylogenetic inference, as analyses performed under alternative cost matrices can produce widely different hypotheses of relationships. To evaluate the effect of varying alignment parameter values on cladogram topology, independent analyses of the complete data set were performed for a range of parameter combinations (sensitivity analysis sensu ) under parsimony. Sensitivity analysis allows discerning between stable relationships (those that are recovered under all or most parameter combinations) and unstable relationships (those that appear only under specific parameter combinations). Twelve parameter combinations (metric transformation step-matrices) were used in the analysis: indel/substitution ratios of 1, 2, and 4; and Tv/Ts ratios of 1, 2, 4, and ∞. When the Tv/Ts cost ratio was other than one, the insertion-deletion cost was set relative to the cost of transversions. Transversions were never given a higher cost than indels. To account for a likely possibility that insertions and deletions spanning multiple contiguous nucleotide positions could have been accommodated by single events, additional sets of parameters taking into account affine indel (gap extension) costs  were carried out. These analyses explored the indel-substitution ratios of 1, 2, and 4, and Tv/Ts ratios of 1, 2, 4, where the extension gap cost was set at a constant minimum (half the cost for transitions). This corresponded to five ratios of gap opening/gap extension costs: 2, 4, 8, 16, and 32. In addition, a cost regime that maximizes homology of both sequence fragments and individual nucleotide positions in the analysis of sequences of variable length  was also examined. This weighting scheme, based on the view of parsimony as a two-taxon analysis , corresponds to the following combination of costs: 2 for substitutions, 3 for gap opening, and 1 for gap extension . In total, 22 parameter combinations were analyzed. The results of the sensitivity analysis are shown as binary plots (Tv/Ts ratio on horizontal and indel/substitution ratio on vertical axes) to designate presence or absence of every clade recovered in the analysis of the complete data set under equal-costs regime. In addition, these results are summarized as a stability tree-a consensus (strict and majority-rule) of clades recovered under the entire parameter space explored. Despite the fact that character and topological congruence, as measured by the ILD  and the topological ILD (TILD; ) respectively, has been proposed as a criterion for choosing among alternative weighting schemes, these measures are partition-dependent and their values are not comparable across different data matrices . Because of the lack of such an objective criterion to decide among alternative weighting schemes, results from equal costs were preferred. Results under additional parameter value combinations were used to assess clade stability.
DNA sequence divergence
A detailed description of DNA sequence divergence patterns is provided in additional file 1: DNA sequence divergence. As expected, the average levels and the range of divergence, based on the estimates of p distance (uncorrected for multiple hits), increased with relative taxonomic rank and, when compared across loci, were the smallest for the 18S and largest for the 16S sequences. With regard to the taxonomically problematic Pinctada imbricata/fucata/radiata species complex, even though none of the markers could provide unambiguous cut-off levels for intra- vs. interspecific sequence divergence, in all cases the levels of divergence in pairwise comparisons between P. imbricata, fucata, and radiata exemplars were invariably lower compared to other interspecific comparisons, and were the same or marginally exceeding the limits of the intraspecific sequence divergence range inferred for other species within Pinctada.
Nucleotide base composition
Nucleotide base composition.
Patterns of nucleotide substitution
The entropy-based statistical test  of the combined molecular data set showed no significant net effect of saturation (Iss < Iss.c; p < 0.05). It revealed that the 18S and H3 sequences were unaffected by multiple hits (Iss < Iss.c; p < 0.05), but suggested the presence of substantial substitution saturation in the 16S sequence (Iss > Iss.c; p < 0.05). Saturation of the 28S sequences can potentially become problematic when extremely asymmetrical topologies are considered (Iss > Iss.cAsym; p < 0.05), which are probably unrealistic given the results of the phylogenetic analysis (see below).
The overall value of the shape parameter α of the gamma distribution was 0.51, suggesting extensive heterogeneity in substitution rates across sites. There was a considerable disparity in the levels of α across loci: the highest level of across-site variation was found in 18S (α = 0.37), followed by H3 (α = 0.58), 28S (α = 0.86), and 16S (α = 1.66). It is noteworthy, that all the nuclear loci displayed substantial (L-shaped distributed) variation, whereas the mitochondrial locus showed relatively moderate (bell-shaped distributed) variation in substitution rates among sites. The estimates of α appear to be accurate for such range of α (the standard error is less than 10% of the α value) . In H3 sequences it was likely due to codon bias: virtually no substitutions were inferred for the second position, less than 2% of sites (1.94% Ts and 1.66% Tv) experienced substitutions in the first position, whereas up to roughly 20% (18.33% Ts and 11.95% Tv) of sites in the third position underwent substitution.
Incongruence-Length Difference Tests
The ILD tests performed simultaneously on all four molecular data partitions showed that the complete data set was homogeneous (P = 0.15), suggesting that combining molecular partitions in a phylogenetic analysis was not likely to reduce phylogenetic accuracy. The pairwise ILD tests, revealed, however, that only the rDNA partitions were entirely congruent (18S:28S, P = 0.35; 18S:16S, P = 0.71; 28S:16S, P = 0.99), whereas the H3 data set was congruent with 16S (P = 0.15), but not with the nuclear rDNA loci (18S:H3, P = 0.01; 28S:H3, P = 0.01). Despite the fact that the appropriate threshold of incongruence is not known, it has been argued that a significance threshold of 0.05 might be too conservative for the ILD test [110, 111]. Given the overall homogeneity of the combined data and marginal incongruence of H3 data, the data-set incongruence was not likely to render an analysis of the combined data misleading. Consequently, the phylogenetic inference based on the combined data was the preferred description of pterioidean relationships, but one must be cautious when interpreting the results with regard to the contribution of the H3 data. The ILD tests together with phylogenentic analyses of individual data partitions and the assessment of their relative contribution to support on a combined-data cladogram (measured by PBrS values) were used to assess the distribution, nature, and extent of agreement among data sets.
Combined analyses of molecular data
The phylogenetic analyses of individual molecular data partitions resulted in cladograms that differ in topology, degree of resolution, and relative support measures. However, all the analyses invariably recovered the Pterioidea and major genus-level clades monophyletic. (For detailed discussion of partitioned analyses of molecular data see additional file 2: Partitioned analyses.)
Combined analyses of morphological and molecular data
A parsimony analysis of the combined morphological and the reduced molecular data sets (hereafter referred to as the "combined reduced data set") performed under equal-costs regime produced a single, highly supported tree (L = 3425, CI = 68.85, RI = 66.14; Figure 9c). When compared to the tree generated for the reduced (molecular-only) data set analyzed under the same conditions, the addition of morphological data reconstituted monophyletic the Pterioidea by placing Pulvinites exempla at the base of the pterioidean subtree; the placement of the remaining taxa was identical. Similarly, the arrangements of pterioidean genera in the analyses of the combined reduced and complete molecular data sets were identical with the only significant topological difference being the identity of the immediate pterioidean sister-group: the Pinnoidea in the former and the Ostreoidea in the latter.
Paired-sites tests of alternative hypotheses of pterioidean sister group.
Paired-sites tests P values
Reliability of phylogenetic inference
The present study provides the first explicit hypothesis for higher-level phylogeny and species-level relationships for the bivalve superfamily Pterioidea based on DNA sequence data.
Nearly complete species-level taxon and character coverage suggest that the random error associated with sampling was not likely to compromise the fidelity of the results inasmuch as supraspecific relationships are concerned. Uncertainty in species-level relationships does, however, remain, due to incomplete taxon sampling, differences in character sampling among congeneric individuals, and potentially insufficient phylogenetic signal of chosen markers for resolving recent divergences. Sequence alignment was straightforward and unambiguous for the protein-coding gene. For the ribosomal sequences, the effect of the uncertainty in nucleotide positional homology on stability of inferred relationships was evaluated using the sensitivity analysis, which allowed for recognizing specific parts of the phylogeny affected by the uncertainty in nucleotide homology and evaluating the extent of its effect.
Nucleotide base composition was nearly perfectly stationary across taxa overall as well as for individual loci, without evidence of taxon attraction due to similar nucleotide-composition bias (e.g., [112, 113]).
Substitution saturation in DNA sequences can potentially underestimate the actual amount of evolutionary change and reduce the phylogenetic signal due to excessive multiple hits in the same nucleotide positions resulting in extensive homoplasy (e.g., ). Despite the fact that extensive saturation was detected for transitions in the 16S sequence, its effect on the phylogenetic inference was negligible, as shown by (1) comparison of the results from individual data partitions, (2) incorporating the Ts/Tv into phylogenetic analysis, (3) character congruence among data partitions, and (4) consistency in the distribution of BrS values. Furthermore, excluding 16S data from the analysis resulted in a decreased resolution and support throughout the tree. These results are consistent with theoretical and empirical findings suggesting that homoplasy does not necessarily confound phylogenetic inference [114–117] and that a given site, which is homoplastic in a sub-part of the most-parsimonious tree, can bring phylogenetic information for another sub-part of the same tree .
Heterogeneity in substitution rates among sites within a nucleotide sequence can have considerable impact on sequence divergence [56, 119–121]. Substantial heterogeneity in substitution rates among lineages resulting in long-branch attraction is another source of misleading inference in molecular data [122, 123]. The agreement between the results of the maximum likelihood analysis under the model allowing for variable base frequencies and parsimony suggested that the predominance of transitions and among-site heterogeneity for most loci, as well as among-lineage heterogeneity in nucleotide substitution rates (implied by the differences in branch lengths) were not likely to be a source of misleading inference. The absence of long-branch attraction despite considerable differences in branch lengths was consistent with prior observation that extensively sampled phylogenies are not sensitive to this artifact [124, 125].
The doubly uniparental inheritance (DUI) , which has been reported for a number of bivalve species , can potentially affect the accuracy of phylogenetic reconstruction due to varying degrees of divergence and homogenization between conspecific genomes. Within the subclass Autolamellibranchiata, the instances of DUI were reported only from the most basal extant group, Mytiloida. Even though the lack of reported instances of DUI in a particular group does not necessarily imply that it is not present, the absence of strict dioeciousness in the Pterioidea suggests that DUI was not a likely to be a problem. All pterioidean species for which reproductive strategies have been elucidated (mostly members of the genera Pinctada and Pteria), are rhythmical protandrous hermaphrodites, with occasional instances of protogyny and simultaneous hermaphroditism, and mtDNA appears to be maternally inherited .
Simultaneous analysis of a single data matrix combining independent character sets potentially increases the descriptive efficiency and explanatory power , provides the basis for evaluating the relative support and taking into account the hidden support provided by individual partitions , and is less sensitive to sampling bias . However, the incongruence among data partitions may indicate that they have evolved under different models of evolution and render a combined-data analysis misleading . Despite topological differences obtained in the analyses of individual data partitions, the results of ILD tests showed that the data sets were largely congruent, implying that a single phylogeny underlies the relationships inferred from individual data partitions. Differences in substitution rates across sites, the average pairwise sequence divergence values, the distribution and levels of support (expressed in PBrS values), and the extent of resolution obtained in the analyses of individual partitions indicated that the marker loci collectively encompassed sufficiently broad spectrum of DNA sequence divergence to produce a nearly completely resolved and well-supported tree. These results also suggested that topological differences among data partitions were probably due to characters that evolved rapidly to provide a reliable signal for sub-terminal (recent) nodes of a tree, but produced noise for the resolution of deeper (ancient) nodes. The overall increased resolution and support of the combined-data trees when compared to the results of partitioned analyses strongly speak for the simultaneous analysis approach.
In summary, the present molecular sequence data and the choice of methodology adequately account for sampling biases and potentially confounding (for phylogenetic inference) effects of various molecular evolutionary processes, providing a strong foundation for accurate, reliable, and robust reconstruction of phylogenetic relationships of the Recent Pterioidea.
Phylogeny of the Pterioidea
The present study corroborates the monophyly of the superfamily Pterioidea and definitively rejects that of all nominal pterioidean families (with the exception of the monotypic Pulvinitidae). Whereas the non-monophyly of some traditional pterioidean groups was anticipated by prior studies [15, 17–19], the arrangement of the genera was novel and unexpected, as well as resolved and strongly supported.
In terms of taxonomic congruence with morphological studies, the analysis of molecular data offered a considerably different phylogenetic hypothesis. Generally assumed close relatedness of commercially important genera Pteria and Pinctada was rejected by the molecular evidence, which was not entirely surprising given the absence of unambiguously optimized non-homoplastic characters supporting the sister-group relationship of these taxa . The presumed close relatedness of the genera Malleus and Isognomon, implied by superficial resemblance in shell morphology and similar life habits [133–135], was also contradicted by the molecular data. The only morphological character supporting a close relatedness of these two genera-the absence of food grooves on inner demibranchs of the gills-is symplesiomorphic in the context of the DNA based topology, as this condition has been also reported from other autolamellibranchiate taxa (e.g., Pectinidae and Limidae; ). Contrary to previously proposed hypothesis [15, 137], this study rejected a close affinity of Isognomon and Pulvinites, placing the latter at the base of the pterioidean tree. This finding was corroborated by the fact that in the morphology-based analysis (Figure 9a) the sister-group relationship of the two genera was weakly supported and relied on a unique combination of shared homoplastic characters (presence of the multivincular ligament, absence of the pallial fold, and serial tissue fusion of the distal edges of the demibranchs).
The present analysis provided the first molecular evidence for a peculiar clade, recently recognised on morphological grounds (Figure 9a) , that consists of relatively understudied, low-diversity genera Electroma, Vulsella, and Crenatula, that were traditionally placed in Pteriidae, Malleidae, and Isognomonidae respectively. The arrangement among the genera, however, varied between the two studies. In the morphology-only analysis, where each genus was represented by a single exemplar, Electroma was basal to Vulsella and Crenatula, the sister-group relationship between which was implied by the reduction of the pedo-byssal apparatus. Instead, in the molecular analysis, Vulsella appeared basal to the Electroma clade that nested the sole representative of Crenatula, rendering Electroma paraphyletic. An unanticipated discovery of polyphyletic Electroma requires detailed morphological and taxonomic reappraisal of this poorly known genus. Another species of Electroma, typically placed in its own subgenus Pterelectroma, E. (P.) physoides, invariably grouped with the Pteria clade, putting into question the taxonomic status of this subgenus.
Due to high sensitivity to alignment parameters and taxon sampling, uncertainty remains regarding the identity of the sister group of the Pterioidea. The paired-sites tests, applied to the alternative topologies differing only in the placement of the outgroup taxa, showed that the trees were not significantly different. Consequently, the sister-group of the Pterioidea could not be unequivocally inferred in light of the present results. Based on the results of the combined-data analyses under uniform weighting and predominant support (in terms of the number of non-homoplastic morphological apomorphies), the Ostreoidea is tentatively proposed here as the most likely pterioidean sister group.
Implications for homology of morphological characters
It has long been acknowledged that extensive homoplasy is a recurrent theme in bivalve phenotypic evolution [138–142] that can potentially mislead phylogenetic inference based on morphological data alone. Optimizing morphological character state transformations onto topology derived from the analysis of molecular data provides means to discern putative homologies and instances of homoplasy. The molecular analyses presented here have confirmed a number of suspected convergences identified on the basis of morphology, but also uncovered a number of hitherto unanticipated ones. The hypotheses of homology of several key characters (that have been considered phylogenetically significant in the Pterioidea as well as in other bivalves) were evaluated in light of a robust phylogenetic hypothesis based on molecular evidence.
A duplicated outer fold of the mantle edge (a "four-fold" condition) has been considered a derived trait that evolved twice independently in the Pterioidea based on the analysis of morphological data  and in agreement with presumably "primitive" three-fold arrangement [143–146]. In contrast, molecular data suggested that the four-fold condition was primitive in the Pterioidea, whereas the three-fold condition was a result of a single reversal to the three-fold condition exhibited by the outgroup taxa. This finding was not entirely unexpected, given the fact that analogous transitions in mantle evolution had occurred in other bivalve lineages .
In the analysis of morphological data, homorhabdic ctenidia (simple gills characterized by a single type of filaments) evolved once from heterorhabdic ctenidia (that contain ordinary and apical filaments). Molecular results, on the other hand, implied that the gill grades had evolved iteratively and the ancestral condition could not be unequivocally resolved. The presence of food grooves in the outer demibranchs showed the same pattern.
The loss of postlarval byssus and posterior pedo-byssal retractor muscles has been previously considered as evidence for sister-group relationship of Vulsella and Crenatula . Both features are likely to be adaptations for living inside sponges, the habit shared by members of the two genera, where physical stabilization is achieved by the attachment to the host sponge. The relationships inferred from the molecular data invariably grouped Crenatula with Electroma, a relationship supported by a single unambiguously optimized nonhomoplastic apomorphy: a T-shaped (in cross-section) typhlosole, a longitudinal fold of the intestine. Molecular results were ambiguous with regard to the immediate relatedness of the Vulsella and the Crenatula/Electroma clades due to alignment uncertainty, and suggested a possibility that the evolution of adaptation for living inside sponges could have been two separate events. This supposition is corroborated by prior ecological observations that the host specificity, and the nature of mutualistic association of Vulsella and Crenatula species with their demosponge hosts are different: the former is a facultative mutualist with keratosid sponges, whereas the latter is an obligatory mutualist with monaxonid sponges [147, 148]. Species of Vulsella possess a relatively thick and elongated shell with an extremely abbreviated hinge line and a narrow prismatic margin that provide a rigid "endo-skeleton" for the sponge, hence facilitating the host's growth. Species of Crenatula, on the other hand, have a very thin shell with a very wide prismatic margin, which appears to be influenced by the sponge growth, and produce highly irregular shell shapes without consistent orientation. The particular form of the multivincular ligament of Crenatula allows for curvature of the extensive hinge line, which facilitates attachment along the hinge line to irregular surfaces. The loss of postlarval byssus in distantly related Malleus albus (not included in the analysis of morphological data) also supports the likelihood of convergence.
The symmetry and relative placement of abdominal sense organs (ASOs), paired mechanoreceptors typically found on the surface of the adductor muscle, have been previously shown to be phylogenetically informative within Autolamellibranchiata [149, 150] and, specifically, within the Pterioidea . In the morphology-based analysis, the clustering of the ASOs around the anus was inferred as a primitive condition in the Pterioidea (found in both ostreid and pinnid outgroup taxa), whereas the dorsal displacement of the right ASO had occurred twice. According to the results of the molecular character analysis, both aspects of the ASO position had evolved twice.
A set of characters that has historically been used for higher-level systematics of pterioidean and other autolamellibranchiate taxa is associated with the types of ligament and their support structures. According to the molecular-based topology, the multivincular ligament characterizes three distantly related genera: Pulvinites, Isognomon, and Crenatula. Morphological data alone also identified an independent origin of multivincular ligament in Crenatula, but suggested a sister-group relationship of Pulvinites and Isognomon on the basis of shared ligament morphology and two other homoplastic characters. It is noteworthy that despite apparent similarity between multivincular systems in Pulvinites and Isognomon, the pattern of ligostracum deposition and the ontogenetic sequence of origination of ligamental layers along the hinge line differ between the genera. Even though not entirely congruent, the results of the molecular and morphological studies reject the long-standing assumption of close relatedness based on a single origin of multivincular ligament in the Pterioidea.
The present molecular evidence confirmed the taxonomic significance of the shape of the anal funnel, an ear-shaped membranous structure situated at the posterior extremity of the rectum that presumably facilitates expulsion of fecal pellets. The absence of the anal funnel in Pulvinites is consistent with its basal placement in the Pterioidea as the same condition is displayed by the outgroup taxa. In contrast, in the analysis based on morphological data, the lack of the funnel was inferred as a loss. The molecular and morphological analyses agree that the anal funnel is subtriangular in outline in the more basal pterioidean clades, whereas it is characteristically lanceolate and rounded in two most derived clades, Pinctada and Vulsella/Crenatula/Electroma, respectively.
Given the uncertainty in the identity of pterioidean sister group, it is instructive to explore the effect of alternative combinations of outgroup taxa on the distribution of diagnostic morphological characters using the best available hypothesis of the ingroup relationships. To this end, morphological characters were optimized on three trees constrained to the identical arrangement of the ingroup taxa (corresponding to that obtained in the analysis of the combined reduced data set under uniform weighting) but differing in the placement of the outgroups.
The Pinnoidea(Ostreoidea/Pterioidea) relationship (L = 330, CI = 0.52, RI = 0.53) was defined by five unambiguously optimized, non-homoplastic apomorphic characters that remained unchanged above this node: (1) the descending intestine produced towards the posteroventral side of the posterior adductor muscle; (2) the loss of the anterior adductor muscle (monomyary); (3) the absence of the pseudonymphae; (4) the presence of a resilifer throughout ontogeny; and (5) the placement of the posterior adductor muscle entirely within the boundary of the inner shell layer. Previously, Steiner and Hammer  had mapped a set of morphological characters on to their maximum likelihood tree substantiating their finding of ostreoidean/pterioidean sister-group relationship by two characters: the monomyary and the presence of the anal funnel. The present study confirmed the monomyaryan condition as a synapomorphy of the clade, but not the occurrence of the anal funnel in different superfamilies, interpreted here as a result of independent origins, as was previously suggested on the basis of morphological data [15, 22]. The Ostreoidea(Pinnoidea/Pterioidea) relationship (L = 334, CI = 0.51, RI = 0.52) was defined by three apomorphic characters: (1) the absence of the marginal mantle lobe fusion; (2) the absence of the eulaterofrontal cirri of gill filaments; and (3) the ascending intestine not produced anteriorly passed the stomach. The Pterioidea(Ostreoidea/Pinnoidea) relationship (L = 333, CI = 0.52, RI = 0.52) was defined by two apomorphic characters: (1) the absence of the ciliated discs on gill filaments and (2) the clustering of ducts of the digestive diverticula. Given comparable levels of homoplasy and the lack of a priori criteria to differentially weigh the characters supporting each of the possibilities, the arrangement supported by the largest number of apomorphies and yielding the shortest tree length, that is (Pinnoidea(Ostreoidea/Pterioidea)), is the preferred hypothesis of relationship.
Species-level taxonomy of Pinctada
Despite the fact that the focus of the present study was to establish higher-level relationships within the Pterioidea, it provided significant insights into species-level taxonomy of the genus Pinctada, a commercially important and the most exhaustively sampled group.
The present study suggests that Pinctada imbricata, P. fucata, and P. radiata are distinct genealogical units. The taxonomic status of the P. imbricata/fucata/radiata species complex previously remained unsettled due to extensive variation in shell characters within and among populations, extremely wide geographical distribution, and transport and hybridization by humans . Traditionally, three distinct species were recognized corresponding to three biogeographic realms: P. imbricata in the western Atlantic region, P. radiata in the eastern Indian Ocean and the Red Sea regions, and P. fucata in the Indo-Pacific region. The Japanese populations have frequently been regarded as a distinct species, P. martensii, or a subspecies, P. fucata martensii. Because of its major role in perliculture, the species complex had become a major research focus in recent years. A large number of comparative genetic analyses using allozyme and DNA sequence data indicated significant levels of gene flow over large geographic distances among populations of Indian Ocean and Indo-Pacific regions, resulting in low levels of genetic differentiation [8, 32]. The pattern of genetic differentiation among the Chinese, Japanese, and Australian populations using amplified fragment length polymorphism (AFLP) markers was consistent with isolation by distance [151, 152]. Shell morphometric studies [153, 154], mating experiments , and comparative karyotype analyses [156–158] failed to establish unequivocal species delineations. To date, no diagnostic discrete morphological characters have been identified for populations from the three geographical regions.
The present results showed shallow levels of divergence among the members of the P. imbricata/fucata/radiata species complex, comparable to the levels of divergence of conspecific exemplars of other Pinctada species. However, the three groups were reciprocally monophyletic showing an apparent clinal geographical structure. Therefore, it might be meaningful to treat these individual populations as evolutionary significant units (ESUs). Taking into account the comparatively low divergence values and the lack of diagnostic morphological characters distinguishing these groups, from the taxonomic standpoint it is advocated here to provisionally recognize them at a subspecies level under the senior synonym, P. imbricata (as Pinctada imbricata imbricata, P. imbricata fucata, and P. imbricata radiata). The final word on the taxonomic status of these taxa will depend on the future population-level analysis with dense sampling throughout the entire distribution range and using genetic markers more sensitive for resolving recent divergencies.
This study also suggested that Pinctada albina and P. nigra, generally distinguished by shell color (as their names imply), represent two colormorphs of the same species. This possibility has been previously suggested based on extremely low levels of genetic divergence between two exemplars of P. albina and one of P. nigra . This finding was consistent with other molecular studies that invariably resolved these species (represented by single exemplars) as sister taxa [159–161]. The present analysis contained three exemplars of each colormorph that were always recovered as a monophyletic group and never formed separate clades diagnosed by color.
In addition, based on the fact that P. mazatlanica invariably nested among representatives of P. margaritifera or members of both species formed an unresolved clade, the present study provides preliminary support for conspecificity of these two species. These findings need to be investigated further and cannot be definitively tested given the present sample size.
The most significant conclusion from the phylogenetic analyses presented here is that the state of pterioidean systematics is no longer in chaos. The present results establish a solid-however unconventional- framework for the higher-level taxonomy of the group, focusing future revisionary systematic effort and providing a better grasp of standing alpha-diversity. The phylogeny is crucial for understanding processes and patterns of diversification and morphological evolution of the Pterioidea through time. To this end, the major future challenge lies in integrating the knowledge on the Recent pterioideans with information on the extensive, well-documented fossil record of the group. As throughout their history, pterioideans remain a globally distributed, relatively common group of bivalves found in most warm, shallow marine environments around the globe, and are likely to display patterns of diversity typical of other marine benthic macrofauna. Therefore, the insights gained from the phylogenetically-informed studies of pterioidean bivalves might be broadly applicable across marine invertebrates.
I would like to thank friends and colleagues around the world who donated or loaned specimens: R. Bieler [Field Museum of Natural History, Chicago, U.S.A. (FMNH)], A.J. Baldinger [Museum of Comparative Zoology, Harvard University, Boston, U.S.A. (MCZ)], P. Bouchet [Muséum National d'Histoire Naturelle, Paris, France (MNHN)], J. Gerber (FMNH), G. Giribet (MCZ), L. Groves [Los Angeles County Museum, Los Angeles, U.S.A. (LACM)], M.G. Harasewych [National Museum of Natural History, Smithsonian Institution, Washington, D.C., U.S.A. (USNM)], D. Herbert (Natal Museum, Pietermaritzburg, South Africa), K. Holmes [American Museum of Natural History, New York, U.S.A. (AMNH)], Japan Pearl Exporters, M. Knapp (University of Vienna, Austria), K.V. Ramana Murty (Andhra University, India), E. Kools (California Academy of Sciences, San Francisco, U.S.A.), P. Maestrati (MNHN), B. Marshall (Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand), P.G. Oliver (National Museum of Wales, Cardiff), C.J.M. Lodeiros Seijo (Instituto Oceanográfico de Venezuela, Universidad de Oriente, Venezuela), R. Shearer (Florida, U.S.A.), L.R. Simone (Museu de Zoologia da Universidade de São Paulo, Brazil), A. Tommasi (Porto Santo Stefano, Italy), K. Umadevi (Andhra University, India), Á. Valdés (LACM), N. Voss (Rosenstiel School of Marine and Atmospheric Science, University of Miami, Florida, U.S.A.), and R.C. Willan (Museum and Art Gallery of the Northern Territories, Darwin, Australia). G. Steiner (University of Vienna, Austria) and T. Masaoka (National Research Institute of Aquaculture, Japan) provided information on specimens, sequences of which were deposited in GenBank. I am indebted to E. Arizmendi Castillo (Perlas del Mar de Cortés, Mexico) for providing assistance during my visit of Guaymas, Mexico in 2003. R. Rorandelli, F. Bartolini, M. Fusi, M. Vannini (all then at Università degli Studi di Firenze, Florence, Italy), and M. Gomei (IUCN Centre for Mediterranean Cooperation, Malaga, Spain) have provided invaluable help during fieldwork in the Tyrranean Sea in Summer 2005. I would like to thank all participants of the Second International Marine Bivalve workshop (Chantaburi, Thailand, 21 August-04 September 2005) and C. Printrakoon (Mahidol University, Bangkok, Thailand) in particular for partnership during the workshop and continuing collaboration. R. DeSalle (AMNH) generously made available molecular laboratory resources at the Sackler Institute for Comparative Genomics. W.C. Wheeler (AMNH) granted access and logistical support for using the parallel computing cluster. M. Leslie (AMNH) provided invaluable help for the laboratory component of the project. M. Coppolino and S. Watson assisted with the American Museum of Natural History mollusk collection. Y. Iwasaki (AMNH) had assisted with translations from Japanese. F. Almeida, A. Varón, M. Weksler (all AMNH), and X. Xia (University of Ottawa, Canada) made technical suggestions. P.M. Mikkelsen (Paleontological Research Institution, Ithaca, U.S.A.), E. Strong (USNM), J. Hammock (USNM), and three anonymous reviewers provided critical suggestions for improving the manuscript. Partial funding toward completion of this work was provided by NSF-PEET Marine Bivalve Project DEB-9978119 (to R. Bieler and P.M. Mikkelsen), NSF Dissertation Improvement Grant DEB-0508311, AMNH Annette Kade Graduate Fellowship, The Conchologists of America Grant, and NSF-AToL Bivalve Tree of Life Project DEB-0732854/0732903/0732860 (to R. Bieler, G. Giribet, and P.M. Mikkelsen).
- Donkin RA: Beyond price. Pearls and pearl-fishing: origins to the Age of Discoveries. 1998, Philadelphia: American Philosophical Society, 224:Google Scholar
- Landman NH, Mikkelsen PM, Bieler R, Bronson B: Pearls: a natural history. 2001, New York: Harry N. Abrams, IncGoogle Scholar
- Strack E: Pearls. 2006, Stuttgart: Ruhle-Diebener-Verlag GmbH & CoGoogle Scholar
- Southgate PC, Lucas JS: The pearl oyster. 2008, Amsterdam, Boston, Heidelberg, London, New York, Oxford, Paris, San Diego, San Francisco, Singapore, Sydney, Tokyo: ElsevierGoogle Scholar
- Burch BL: Pearly shells - part 5: transport by man of commercial pearl shells and their hitch-hikers. Hawaiian Shell News. 1995, 43 (6): 3-6.Google Scholar
- Borrero FJ, Díaz JM: Introduction of the Indo-Pacific pteriid bivalve Electroma sp. to the tropical western Atlantic. Bull Mar Sci. 1998, 62 (1): 269-274.Google Scholar
- O'Connor WA, Gifford SP: Environmental impacts of pearl farming. The pearl oyster. Edited by: Southgate PC, Lucas JS. 2008, Amsterdam, Boston, Heidelberg, London, New York, Oxford, Paris, San Diego, San Francisco, Singapore, Sydney, Tokyo: Elsevier, 497-525. full_text.Google Scholar
- Wada KT, Jerry DR: Population genetics and stock improvement. The pearl oyster. Edited by: Southgate PC, Lucas JS. 2008, Amsterdam, Boston, Heidelberg, London, New York, Oxford, Paris, San Diego, San Francisco, Singapore, Sydney, Tokyo: Elsevier, 437-471. full_text.Google Scholar
- Westbroek P, Marin F: A marriage of bone and nacre. Nature. 1998, 392: 861-862. 10.1038/31798.PubMedGoogle Scholar
- Milet C, Berland S, Lamghari M, Mouries L, Jolly C, Borzeix S, Doumenc D, Lopez É: Conservation of signal molecules involved in biomineralisation control in calcifying matrices of bone and shell. C R Palevol. 2004, 3: 493-501. 10.1016/j.crpv.2004.07.010.Google Scholar
- Gray JE: List of the genera of Recent Mollusca, their synonyma and types. Proc Zool Soc London. 1847, 15 (178): 129-219.Google Scholar
- Newell ND, et al: Superfamily Pteriacea Gray, 1847 (1820). Treatise on Invertebrate Paleontology Part N Mollusca 6: Bivalvia. Edited by: Cox LR, Newell ND, Boyd DW, Branson CC, Casey R, Chavan A, Coogan AH, Dechaseaux C, Fleming CA, Haas F. 1969, Lawrence, Kansas: Geological Society of America and University of Kansas, 1: N297-Google Scholar
- Boss KJ: Mollusca. Synopsis and classification of living organisms. Edited by: Parker SP. 1982, New York: McGraw-Hill, 1: 945-1166.Google Scholar
- Butler AJ: Order Pterioida. Mollusca: the southern synthesis Fauna of Australia. Edited by: Beesley PL, Ross GJB, Wells A. 1998, Melbourne: CSIRO Publishing, 5: 261-267. Part AGoogle Scholar
- Tëmkin I: Morphological perspective on classification and evolution of Recent Pterioidea (Mollusca: Bivalvia). Zool J Linn Soc. 2006, 148 (3): 253-312. 10.1111/j.1096-3642.2006.00257.x.Google Scholar
- Jackson RT: Phylogeny of the Pelecypoda: the Aviculidae and their allies. Mem Boston Soc Nat Hist. 1890, 4: 277-400.Google Scholar
- Matsumoto M: Phylogenetic analysis of the subclass Pteriomorphia (Bivalvia) from mtDNA COI sequences. Mol Phylogenet Evol. 2003, 27: 429-440. 10.1016/S1055-7903(03)00013-7.PubMedGoogle Scholar
- Steiner G, Hammer S: Molecular phylogeny of the Bivalvia inferred from 18S rDNA sequences with particular reference to the Pteriomorphia. The evolutionary biology of the Bivalvia. Edited by: Harper EM, Taylor JD, Crame JA. 2000, London: Geological Society, 11-29. vol. Special Publications, 177Google Scholar
- Giribet G, Distel DL: Bivalve phylogeny and molecular data. Molecular systematics and phylogeography of mollusks. Edited by: Lydeard C, Lindberg DR. 2003, Washington and London: Smithsonian Books, 45-90.Google Scholar
- Pojeta J: The origin and early taxonomic diversification of pelecypods. Philos Trans R Soc, B. 1978, 284: 225-246. 10.1098/rstb.1978.0065.Google Scholar
- Waller TR: Morphology, morphoclines and a new classification of the Pteriomorphia (Mollusca: Bivalvia). Philos Trans R Soc, B. 1978, 284: 345-365. 10.1098/rstb.1978.0072.Google Scholar
- Waller TR: Origin of the molluscan class Bivalvia and a phylogeny of major groups. Bivalves: an eon of evolution - paleobiological studies honoring Norman D Newell. Edited by: Johnston PA, Haggart JW. 1998, Calgary: University of Calgary Press, 1-45.Google Scholar
- Cope JCW: The early evolution of the Bivalvia. Origin and evolutionary radiation of the Mollusca. Centenary Symposium of the Malacological Society of London. Edited by: Taylor JD. 1996, Oxford, New York: Oxford University Press, 361-370.Google Scholar
- Giribet G, Wheeler WC: On bivalve phylogeny: a high-level analysis of the Bivalvia (Mollusca) based on combined morphology and DNA sequence data. Invertebr Biol. 2002, 121 (4): 271-324. 10.1111/j.1744-7410.2002.tb00132.x.Google Scholar
- Adamkewicz SL, Harasewych MG, Blake J, Saudek D, Bult CJ: A molecular phylogeny of the bivalve mollusks. Mol Biol Evol. 1997, 14 (6): 619-629.PubMedGoogle Scholar
- Campbell DC: Molecular evidence on the evolution of the Bivalvia. The evolutionary biology of the Bivalvia. Edited by: Harper EM, Taylor JD, Crame JA. 2000, London: The Geological Society, 177: 31-46.Google Scholar
- Matsumoto M: Molecular phylogenetic analysis of pteriomorph bivalves. Unpublished Ph.D. dissertation. 2001, Yokohama, Japan: Kanagawa UniversityGoogle Scholar
- Márquez-Aliaga A, Jiménez-Jiménez AP, Checa AG, Hagdorn H: Early oysters and their supposed Permian ancestors. Palaeogeogr, Palaeoclimatol, Palaeoecol. 2005, 229: 127-136. 10.1016/j.palaeo.2005.06.034.Google Scholar
- Hautmann M: Shell morphology and phylogenetic origin of oysters. Palaeogeogr, Palaeoclimatol, Palaeoecol. 2006, 240: 668-671. 10.1016/j.palaeo.2006.03.006.Google Scholar
- Malchus N: Problems concerning early oyster evolution: a reply to Márquez-Aliaga and Hautmann. Palaeogeogr, Palaeoclimatol, Palaeoecol. 2008, 258: 130-134. 10.1016/j.palaeo.2007.07.006.Google Scholar
- Kirkendale L, Lee T, Baker P, Ó Foighil D: Oysters of the Conch Republic (Florida Keys): a molecular phylogenetic study of Parahyotissa mcgintyi, Teskeyostrea weberi and Ostrea equestris. Malacologia. 2004, 46 (2): 309-326.Google Scholar
- Wada KT, Tëmkin I: Taxonomy and phylogeny. The pearl oyster. Edited by: Southgate PC, Lucas JS. 2008, Amsterdam, Boston, Heidelberg, London, New York, Oxford, Paris, San Diego, San Francisco, Singapore, Sydney, Tokyo: Elsevier, 37-75. full_text.Google Scholar
- Hillis DM, Dixon MT: Ribosomal DNA: molecular evolution and phylogenetic inference. Q Rev Biol. 1991, 66 (4): 411-453. 10.1086/417338.PubMedGoogle Scholar
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410.PubMedGoogle Scholar
- Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093/nar/25.17.3389.PubMed CentralPubMedGoogle Scholar
- Wheeler W: Homology and the optimization of DNA sequence data. Cladistics. 2001, 17: S3-S11. 10.1111/j.1096-0031.2001.tb00100.x.PubMedGoogle Scholar
- Wheeler WC: Homology and DNA sequence data. The character concept in evolutionary biology. Edited by: Wagner GP. 2001, San Diego: Academic Press, 303-317. full_text.Google Scholar
- Varón A, Vinh LS, Bomash I, Wheeler WC: POY 4.1. 2008, New York: American Museum of Natural HistoryGoogle Scholar
- Morrison DA: Multiple sequence alignment for phylogenetic purposes. Aust Syst Bot. 2006, 19: 479-539. 10.1071/SB06020.Google Scholar
- Wheeler WC, Aagesen L, Arango CP, Faivovich J, Grant T, D'Haese C, Janies D, Smith WL, Varón A, Giribet G: Dynamic homology and phylogenetic systematics: a unified approach using POY. 2006, New York: American Museum of Natural HistoryGoogle Scholar
- Wheeler WC: Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search. Cladistics. 2003, 19: 261-268. 10.1111/j.1096-0031.2003.tb00369.x.PubMedGoogle Scholar
- Giribet G: Generating implied alignments under direct optimization using POY. Cladistics. 2005, 21: 396-402. 10.1111/j.1096-0031.2005.00071.x.Google Scholar
- Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al: Clustal W and Clustal X version 2.0. Bioinformatics. 2007, 23: 2947-2948. 10.1093/bioinformatics/btm404.PubMedGoogle Scholar
- Winnepenninckx B, Backeljau T, De Wachter R: Small ribosomal subunit RNA and the phylogeny of Mollusca. Nautilus. 1994, 108 (Suppl 2): 98-110.Google Scholar
- Lydeard C, Holznagel WE, Schnare MN, Gutell RR: Phylogenetic analysis of molluscan mitochondrial LSU rDNA sequences and secondary structures. Mol Phylogenet Evol. 2000, 15 (1): 83-102. 10.1006/mpev.1999.0719.PubMedGoogle Scholar
- Michot B, Hassouna N, Bachellerie JP: Secondary structure of mouse 28S rRNA and general model for the folding of the large rRNA in eukaryotes. Nucleic Acids Res. 1984, 12 (10): 4259-4279. 10.1093/nar/12.10.4259.PubMed CentralPubMedGoogle Scholar
- Michot B, Bachellerie JP: Comparisons of large subunit rRNAs reveal some eukaryote-specific elements of secondary structure. Biochimie. 1987, 69: 11-23. 10.1016/0300-9084(87)90267-7.PubMedGoogle Scholar
- Gutell RR, Fox GE: A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Res. 1988, 16 (Suppl): r175-r269.PubMed CentralPubMedGoogle Scholar
- Wuyts J, De Rijk P, Van de Peer Y, Winkelmans T, De Wachter R: The European large subunit ribosomal RNA database. Nucleic Acids Res. 2001, 29 (1): 175-177. 10.1093/nar/29.1.175.PubMed CentralPubMedGoogle Scholar
- Wuyts J, Van de Peer Y, Winkelmans T, De Wachter R: The European database on small subunit ribosomal RNA. Nucleic Acids Res. 2002, 30: 183-185. 10.1093/nar/30.1.183.PubMed CentralPubMedGoogle Scholar
- Wells D, Brown D: Histone and histone gene compilation and alignment update. Nucleic Acids Res. 1991, 19 (Suppl): 2173-2188.PubMed CentralPubMedGoogle Scholar
- Xia X, Xie Z, Salemi M, Chen L, Wang Y: An index of substitution saturation and its application. Mol Phylogenet Evol. 2003, 26: 1-7. 10.1016/S1055-7903(02)00326-3.PubMedGoogle Scholar
- Xia X, Xie Z: DAMBE: software package for data analysis in Mol Biol Evol. J Hered. 2001, 92 (4): 371-373. 10.1093/jhered/92.4.371.PubMedGoogle Scholar
- Maddison DR, Maddison WP: MacClade. Version 4.07. 2005, Sunderland, MA: Sinauer AssociatesGoogle Scholar
- Swofford DL: PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4.0d105. 2002, Sunderland, MA: SinauerGoogle Scholar
- Yang Z: Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol. 1993, 10 (6): 1396-1401.PubMedGoogle Scholar
- Yang Z: Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol. 1994, 39: 306-314. 10.1007/BF00160154.PubMedGoogle Scholar
- Rzhetsky A, Nei M: A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol. 1992, 9: 945-967.Google Scholar
- Rzhetsky A, Nei M: Statistical properties of the ordinary least-squares, generalized least-squares, and minimum evolution methods of phylogenetic inference. J Mol Evol. 1992, 35: 367-375. 10.1007/BF00161174.PubMedGoogle Scholar
- Lanave C, Preparata G, Saccone C, Serio G: A new method for calculating evolutionary substitution rates. J Mol Evol. 1984, 20: 86-93. 10.1007/BF02101990.PubMedGoogle Scholar
- Tavaré S: Some probabilistic and statistical problems in the analysis of DNA sequences. Lect Math Life Sci. 1986, 17: 57-86.Google Scholar
- Rodriguez F, Oliver JF, Marin A, Medina JR: The general stochastic model of nucleotide substitutions. J Theor Biol. 1990, 142: 485-501. 10.1016/S0022-5193(05)80104-3.PubMedGoogle Scholar
- Akaike H: A new look at the statistical model identification. IEEE Trans Autom Control. 1974, 19: 716-723. 10.1109/TAC.1974.1100705.Google Scholar
- Mickevich MF, Farris JS: The implications of congruence in Menidia. Syst Zool. 1981, 30: 351-370. 10.2307/2413255.Google Scholar
- Farris JS, Källersjö M, Kluge AG, Bult C: Constructing a significance test for congruence. Syst Biol. 1995, 44 (4): 570-572.Google Scholar
- Farris JS, Källersjö M, Kluge AG, Bult C: Testing significance of incongruence. Cladistics. 1995, 10: 315-319. 10.1111/j.1096-0031.1994.tb00181.x.Google Scholar
- Barker FK, Lutzoni FM: The utility of the incongruence length difference test. Syst Biol. 2002, 51: 625-637. 10.1080/10635150290102302.PubMedGoogle Scholar
- Darlu P, Lecointre G: When does the incongruence length difference test fail?. Mol Biol Evol. 2002, 19 (4): 432-437.PubMedGoogle Scholar
- Swofford DL, Olsen GJ: Phylogeny reconstruction. Molecular systematics. Edited by: Hillis DM, Moritz C. 1990, Sunderland, MA: Sinauer, 411-501.Google Scholar
- Wheeler WC: Optimization alignment: the end of multiple sequence alignment in phylogenetics?. Cladistics. 1996, 1-9. 10.1111/j.1096-0031.1996.tb00189.x. 12Google Scholar
- Sankoff D: Minimal mutation trees of sequences. SIAM J Appl Math. 1975, 28: 35-42. 10.1137/0128004.Google Scholar
- Sankoff D, Cedergren RJ: Simultaneous comparison of three or more sequences related by a tree. Time warps, string edits, and macromolecules: the theory and practice of sequence comparison. Edited by: Sankoff D, Kruskal J. 1983, Stanford, CA: CSLI Publications, 253-263.Google Scholar
- Hein J: A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Mol Biol Evol. 1989, 6: 649-668.PubMedGoogle Scholar
- Hein J: A tree reconstruction method that is economical in the number of pairwise comparisons used. Mol Biol Evol. 1989, 6: 669-684.PubMedGoogle Scholar
- Jiang T, Lawler EL, Wang A: Aligning sequences via an evolutionary tree: complexity and approximation. Proceedings of the Twenty-Sixth Annual Symposium on Theory of Computing, STOC 94-5% 94, Montreal, Quebec, Canada: 1994. 1994, 760-769. full_text.Google Scholar
- Sankoff D, Rousseau P: Locating the vertices of a Steiner tree in arbitrary space. Math Program. 1975, 9: 240-246. 10.1007/BF01681346.Google Scholar
- Schwikowski B, Vingron M: The deferred path heuristic for the generalized tree alignment problem. J Comput Biol. 1997, 4: 415-431. 10.1089/cmb.1997.4.415.PubMedGoogle Scholar
- Kluge AG, Farris J: Quantitative phyletics and the evolution of anurans. Syst Zool. 1969, 18: 1-32. 10.2307/2412407.Google Scholar
- Farris JS: Methods for computing Wagner trees. Syst Zool. 1970, 19: 83-92. 10.2307/2412028.Google Scholar
- Nixon KC: The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics. 1999, 15: 407-414. 10.1111/j.1096-0031.1999.tb00277.x.Google Scholar
- Goloboff PA: Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics. 1999, 15: 415-428. 10.1111/j.1096-0031.1999.tb00278.x.Google Scholar
- Wheeler WC: Iterative pass optimization of sequence data. Cladistics. 2003, 19: 254-260. 10.1111/j.1096-0031.2003.tb00368.x.PubMedGoogle Scholar
- Nixon KC, Carpenter JM: On outgroups. Cladistics. 1993, 9: 413-426. 10.1111/j.1096-0031.1993.tb00234.x.Google Scholar
- Stamatakis A: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006, 22 (21): 2688-2690. 10.1093/bioinformatics/btl446.PubMedGoogle Scholar
- Sullivan J, Abdo Z, Joyce P, Swofford DL: Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Mol Biol Evol. 2005, 22 (6): 1386-1392. 10.1093/molbev/msi129.PubMedGoogle Scholar
- Posada D, Crandall KA: MODELTEST: testing the model of DNA substitution. Bioinformatics. 1998, 14 (9): 817-818. 10.1093/bioinformatics/14.9.817.PubMedGoogle Scholar
- Posada D, Buckley TR: Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Syst Biol. 2004, 53: 793-808. 10.1080/10635150490522304.PubMedGoogle Scholar
- Gu X: Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol. 1995, 12: 546-557.PubMedGoogle Scholar
- Yang Z: Computational molecular evolution. 2006, Oxford and New YorkGoogle Scholar
- Sullivan J, Holsinger KE, Simon C: The effect of topology on estimates of among-site rate variation. J Mol Evol. 1996, 42: 308-312. 10.1007/BF02198857.PubMedGoogle Scholar
- Farris JS: The retention index and the rescaled consistency index. Cladistics. 1989, 5: 417-419. 10.1111/j.1096-0031.1989.tb00573.x.Google Scholar
- Bremer K: The limits of amino-acid sequence data in angiosperm phylogenetic reconstruction. Evolution. 1988, 42: 795-803. 10.2307/2408870.Google Scholar
- Farris JS, Albert VA, Källersjö M, Lipscomb D, Kluge AG: Parsimony jackknifing outperforms neighbor-joining. Cladistics. 1996, 12: 99-124. 10.1111/j.1096-0031.1996.tb00196.x.Google Scholar
- Baker RH, DeSalle R: Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Syst Biol. 1997, 46 (4): 654-673.PubMedGoogle Scholar
- Sorenson MD, Franzosa EA: TreeRot, version 3. 2007, Boston, MA: Boston UniversityGoogle Scholar
- Rambaut A: FigTree: tree figure frawing tool version 1.1.2. 2006, Edinburgh: Institute of Evolutionary Biology, University of EdinburghGoogle Scholar
- Kishino H, Hasegawa M: Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol. 1989, 29: 170-179. 10.1007/BF02100115.PubMedGoogle Scholar
- Kishino H, Miyata T, Hasegawa M: Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J Mol Evol. 1990, 30: 151-160. 10.1007/BF02109483.Google Scholar
- Templeton AR: Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and apes. Evolution. 1983, 37 (2): 221-244. 10.2307/2408332.Google Scholar
- Templeton AR: Convergent evolution and nonparametric inferences from restriction data and DNA sequences. Statistical analysis of DNA sequence data. Edited by: Weir BS. 1983, New York: Marcel Dekker, Inc, 151-179.Google Scholar
- Goldman N, Anderson JP, Rodrigo AG: Likelihood-based tests of topologies in phylogenetics. Syst Biol. 2000, 49 (4): 652-670. 10.1080/106351500750049752.PubMedGoogle Scholar
- Nei M, Kumar S: Molecular evolution and phylogenetics. 2000, Oxford: Oxford University PressGoogle Scholar
- Wheeler WC: Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Syst Biol. 1995, 44 (3): 321-331.Google Scholar
- Gotoh O: An improved algorithm for matching biological sequences. J Mol Biol. 1982, 162: 705-708. 10.1016/0022-2836(82)90398-9.PubMedGoogle Scholar
- De Laet J: Parsimony and the problem of inapplicables in sequence data. Parsimony, phylogeny, and genomics. Edited by: Albert VA. 2005, Oxford University Press, 81-116.Google Scholar
- De Laet J, Smets E: On the three taxon approach to parsimony analysis. Cladistics. 1998, 14: 363-381. 10.1006/clad.1998.0075.Google Scholar
- Wheeler WC: Measuring topological congruence by extending character techniques. Cladistics. 1999, 15: 131-135. 10.1111/j.1096-0031.1999.tb00255.x.Google Scholar
- Faith DP, Trueman JWH: Towards an inclusive philosophy for phylogenetic inference. Syst Biol. 2001, 50 (3): 331-350. 10.1080/106351501300317969.PubMedGoogle Scholar
- Takezaki N, Gojobori T: Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences. Mol Biol Evol. 1999, 16 (5): 590-601.PubMedGoogle Scholar
- Sullivan DL: Combining data with different distributions of among-site variation. Syst Biol. 1996, 45: 375-380.Google Scholar
- Cunningham CW: Can three incongruence tests predict when data should be combined?. Mol Biol Evol. 1997, 14 (7): 733-740.PubMedGoogle Scholar
- Lockhart PJ, Steel MA, Hendy MD, Penny D: Recovering evolutionary trees under a more realistic model of sequence evolution. Mol Biol Evol. 1994, 11 (4): 605-612.PubMedGoogle Scholar
- Galtier N, Gouy M: Inferring phylogenies from DNA sequences of unequal base compositions. Proc Natl Acad Sci USA. 1995, 92 (24): 11317-11321. 10.1073/pnas.92.24.11317.PubMed CentralPubMedGoogle Scholar
- Yang Z: On the best evolutionary rate for phylogenetic analysis. Syst Biol. 1998, 47 (1): 125-133. 10.1080/106351598261067.PubMedGoogle Scholar
- Björklund M: Are third positions really that bad? A test using vertebrate cytochrome b. Cladistics. 1999, 15 (2): 191-197.Google Scholar
- Källersjö M, Albert VA, Farris JS: Homoplasy increases phylogenetic structure. Cladistics. 1999, 15: 91-93.Google Scholar
- Wenzel JW, Siddall ME: Noise. Cladistics. 1999, 15: 51-54. 10.1111/j.1096-0031.1999.tb00394.x.Google Scholar
- Philippe H, Lecointre G, Lê HLV, Guyader HL: A critical study of homoplasy in molecular data with the use of a morphologically based cladogram, and its consequences for character weighting. Mol Biol Evol. 1996, 13 (9): 1174-1186.Google Scholar
- Navidi WC, Churchill GA, Haeseler Av: Methods for inferring phylogenies from nucleotide acid sequence data by using maximum likelihood and linear invariants. Mol Biol Evol. 1991, 8: 128-143.PubMedGoogle Scholar
- Yang Z: Phylogenetic analysis using parsimony and likelihood methods. J Mol Evol. 1996, 42: 294-307. 10.1007/BF02198856.PubMedGoogle Scholar
- Kuhner MK, Felsenstein J: A simulation comparison of phylogeny algorithms under equaland unequal evolutionary rates. Mol Biol Evol. 1994, 11: 459-468.PubMedGoogle Scholar
- Felsenstein J: Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool. 1978, 27 (4): 401-410. 10.2307/2412923.Google Scholar
- Hendy MD, Penny D: A framework for the quantitative study of evolutionary trees. Syst Zool. 1989, 38 (4): 297-309. 10.2307/2992396.Google Scholar
- Hillis DM: Inferring complex phylogenies. Nature. 1996, 383: 130-131. 10.1038/383130a0.PubMedGoogle Scholar
- Anderson FE, Swofford DL: Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA. Mol Phylogenet Evol. 2004, 33: 440-451. 10.1016/j.ympev.2004.06.015.PubMedGoogle Scholar
- Zouros E, Ball AO, Saavedra C, Freeman KR: Mitochondrial DNA inheritance. Nature. 1994, 368: 818-10.1038/368818a0.PubMedGoogle Scholar
- Theologidis I, Fodelianakis S, Gaspar MB, Zouros E: Doubly uniparental inheritance (DUI) of mitochondrial DNA in Donax trunculus (Bivalvia: Donacidae) and the problem of its sporadic detection in Bivalvia. Evolution. 2008, 62 (4): 959-970. 10.1111/j.1558-5646.2008.00329.x.PubMedGoogle Scholar
- Saucedo PE, Southgate PC: Reproduction, development and growth. The pearl oyster. Edited by: Southgate PC, Lucas JS. 2008, Amsterdam, Boston, Heidelberg, London, New York, Oxford, Paris, San Diego, San Francisco, Singapore, Sydney, Tokyo: Elsevier, 131-186. full_text.Google Scholar
- Nixon KC, Carpenter JM: On simultaneous analysis. Cladistics. 1996, 12: 221-241. 10.1111/j.1096-0031.1996.tb00010.x.Google Scholar
- Gatesy J, O'Grady P, Baker RH: Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa. Cladistics. 1999, 15: 271-313. 10.1111/j.1096-0031.1999.tb00268.x.Google Scholar
- Cummings MP, Otto SP, Wakeley J: Sampling properties of DNA sequence data in phylogenetic analysis. Mol Biol Evol. 1995, 12: 814-822.PubMedGoogle Scholar
- Bull JJ, Huelsenbeck JP, Cunningham CW, Swofford DL, Waddell PJ: Partitioning and combining data in phylogenetic analysis. Syst Biol. 1993, 42: 384-397.Google Scholar
- Yonge CM: Form and habit in species of Malleus (including the "hammer oysters") with comparative observations on Isognomon isognomon. Biol Bull. 1968, 135: 378-405. 10.2307/1539789.Google Scholar
- Stanley SM: Functional morphology and evolution of byssally attached bivalve mollusks. J Paleontol. 1972, 46 (2): 165-212.Google Scholar
- Seilacher A: Constraint and innovation in bivalve mollusc evolution. Evolution and development Report of the Dahlem Workshop on Evolution and Development, Berlin 1981, Ma9 10-15. Edited by: Bonner JT. 1982, Berlin: Springer, 302-305.Google Scholar
- Atkins D: On the ciliary mechanisms and interrelationships of lamellibranchs. Part 3. Types of lamellibranch gills and their food currents. Q J Microsc Sci. 1937, 79 (315): 375-421.Google Scholar
- Palmer TJ: Revision of the bivalve family Pulvinitidae Stephenson, 1941. Palaeontology. 1984, 27 (Part 4): 815-824.Google Scholar
- Newell ND, Boyd DW: A palaeontologist's view of bivalve phylogeny. Philos Trans R Soc, B. 1978, 284: 203-215. 10.1098/rstb.1978.0063.Google Scholar
- Seilacher A: Constructional morphology of bivalves: evolutionary pathways in primary versus secondary soft-bottom dwellers. Palaeontology. 1984, 27 (2): 207-237.Google Scholar
- Seilacher A: Secondary soft-bottom dwellers: convergent responses to an evolutionary "mistake". Evolving form and function: fossils and development; proceedings of a symposium honoring Adolf Seilacher for his contribution to paleontology, in celebration of his 80th birthday; 2005 Apr 1-2; New Haven. Edited by: Briggs DEG. 2005, New Haven: Peabody Museum of Natural History, Yale University, 257-271.Google Scholar
- Stanley SM: Adaptive themes in the evolution of the Bivalvia (Mollusca). Annu Rev Earth Planet Sci. 1975, 3: 361-385. 10.1146/annurev.ea.03.050175.002045.Google Scholar
- Skelton PW, Benton MJ: Mollusca: Rostroconchia, Scaphopoda and Bivalvia. The fossil record 2. Edited by: Benton MJ. 1993, London: Chapman & Hall, 237-263.Google Scholar
- Yonge CM: Mantle fusion in the Lamellibranchia. Pubbl Stn Zool Napoli. 1957, 29: 151-171.Google Scholar
- Cox LR, et al: General features of Bivalvia. Part N Mollusca 6: Bivalvia. Edited by: Cox LR, Newell ND, Boyd DW, Branson CC, Casey R, Chavan A, Coogan AH, Dechaseaux C, Fleming CA, Haas F. 1969, Lawrence, Kansas: Geological Society of America and University of Kansas, 1: N2-N129.Google Scholar
- Taylor JD, Kennedy WJ, Hall A: The shell structure and mineralogy of the Bivalvia. Introduction. Nuculacea-Trigonacea. Bull Br Mus (Nat Hist), Zool. 1969, 1-125. Suppl 3Google Scholar
- Morton B: Mantle and body cavities. Mollusca: the southern synthesis Fauna of Australia. Edited by: Beesley PL, Ross GJB, Wells A. 1998, Melbourne: CSIRO Publishing, 5 (Part A): 203-204.Google Scholar
- Reid RGB, Porteous S: Aspects of the functional morphology and digestive physiology of Vulsella vulsella (Linné) and Crenatula modiolaris (Lamarck), bivalves associated with sponges. The malacofauna of Hong Kong and Southern China Proceedings of the First International Workshop 23 March - 8 April 1977, Hong Kong. Edited by: Morton B. 1980, Hong Kong: Hong Kong University Press, 291-310.Google Scholar
- Morton B: Partnerships in the sea: Hong Kong's marine symbioses. 1988, Hong Kong: Hong Kong University PressGoogle Scholar
- Haszprunar G: Comparative analysis of the abdominal sense organs of Pteriomorpha (Bivalvia). J Molluscan Stud, Suppl. 1983, 12 (A): 47-50.Google Scholar
- Haszprunar G: The fine structure of the abdominal sense organs of Pteriomorpha (Mollusca, Bivalvia). J Molluscan Stud. 1985, 51 (3): 315-319.Google Scholar
- Yu DH, Chu KH: Species identity and phylogenetic relationship of the pearl oysters in Pinctada Röding, 1798 based on ITS sequence analysis. Biochem Syst Ecol. 2006, 34: 240-250. 10.1016/j.bse.2005.09.004.Google Scholar
- Yu DH, Chu KH: Genetic variation in wild and cultured populations of the pearl oyster Pinctada fucata from southern China. Aquaculture. 2006, 258 (1-4): 220-227. 10.1016/j.aquaculture.2006.03.024.Google Scholar
- Beaurnent AR, Khamdan SAA: Electrophoretic and morphometric characters in population differetiation of the pearl oyster, Pinctada radiata (Leach), from around Bahrain. J Molluscan Stud. 1994, 57: 433-441.Google Scholar
- Colgan DJ, Ponder WF: Genetic discrimination of morphologically similar, sympatric species of pearl oysters (Mollusca: Bivalvia: Pinctada) in eastern Australia. Mar Freshwater Res. 2002, 53: 697-709. 10.1071/MF99178.Google Scholar
- Atsumi T, Komaru A, Okamoto C: Genetic relationship among the Japanese pearl oyster Pinctada fucata martensii and foreign pearl oysters. Fish Genet Breed Sci. 2004, 33: 135-142.Google Scholar
- Wada K: Chromosome karyotypes of three bivalves: the oysters, Isognomon alatus and Pinctada imbricata, and the bay scallop, Argopecten irradians irradians. Biol Bull. 1978, 155: 235-245. 10.2307/1540878.Google Scholar
- Komaru A, Wada KT: Karyotype of the Japanese pearl oyster, Pinctada fucata martensi, observed in the trochophore larvae. Yoshoku Kenkyusho Kenkyu Hokoku (Bull Natl Res Inst Aquacult). 1985, 7: 105-107.Google Scholar
- Wada KT, Komaru A: Karyotypes in five species of the Pteriidae (Bivalvia: Pteriomorphia). Venus. 1985, 44 (3): 183-192.Google Scholar
- Masaoka T, Kobayashi T: Phylogenetic relationships in pearl oysters (Genus: Pinctada) based on nuclear rRNA sequences. DNA Polymorphism. 2002, 10: 100-104.Google Scholar
- Masaoka T, Kobayashi T: Estimation of phylogenetic relationships in pearl oysters (Genus: Pinctada) based on 28SrRNA and ITS sequence. DNA Polymorphism. 2003, 11: 76-81.Google Scholar
- Masaoka T, Kobayashi T: Estimation of phylogenetic relationships in pearl oysters (Mollusks: Bivalvia: Pinctada) used for pearl production based on rRNA genes sequence. DNA Polymorphism. 2005, 13: 151-162.Google Scholar
- Giribet G, Carranza S, Baguna J, Riutort M, Ribera C: First molecular evidence for the existence of a Tardigrada + Arthropoda clade. Mol Biol Evol. 1996, 13 (1): 76-84.PubMedGoogle Scholar
- Park JK, Foighil DO: Sphaeriid and corbiculid clams represent separate heterodont bivalve radiations into freshwater environments. Mol Phylogenet Evol. 2000, 14 (1): 75-88. 10.1006/mpev.1999.0691.PubMedGoogle Scholar
- Kessing B, Croom H, Martin A, McIntosh C, Owen Mcmillan W, Palumbi S: The simple fool's guide to PCR. 1989, Honolulu, Hawaii: University of HawaiiGoogle Scholar
- Colgan DJ, McLauchlan A, Wilson GDF, Livingston SP, Edgecombe GD, Macaranas J, Cassis G, Gray MR: Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution. Aust J Zool. 1998, 46: 419-437. 10.1071/ZO98048.Google Scholar
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